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This criticism also applies to cuffdiff, at least to the version described in the paper. (There is a new version of cuffdiff that allows for biological replicates but there is no documentation on its method yet, and hence it is unclear whether it now asks the relevant question.)
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Hello,
Simon mentioned the existence of a new version of Cuffdiff that allows for biological replicates. Does anyone know anything else about this new version? Will it be released soon or is it already available somewhere?
Given the currently available Cuffdiff version (v0.9.3), is there any viable workaround to analyze groups of samples (e.g. control samples compared with treated samples)?
Thank you,
Alexandra